1GYO

Crystal structure of the di-tetraheme cytochrome c3 from Desulfovibrio gigas at 1.2 Angstrom resolution

Summary for 1GYO

• Entry DOI: 10.2210/pdb1gyo/pdb
• Descriptor: CYTOCHROME C3, A DIMERIC CLASS III C-TYPE CYTOCHROME, HEME C, GLYCEROL, ... (4 entities in total)
• Functional Keywords: electron transport, cytochrome c3, di-tetraheme, ab initio, electron transfer
• Biological source: DESULFOVIBRIO GIGAS
• Total number of polymer chains: 2
• Total formula weight: 29613.95

Authors

Aragao, D.,Frazao, C.,Sieker, L.,Sheldrick, G.M.,Legall, J.,Carrondo, M.A. (deposition date: 2002-04-29, release date: 2002-05-24, Last modification date: 2023-03-29)

Primary citation

Aragao, D.,Frazao, C.,Sieker, L.,Sheldrick, G.M.,Legall, J.,Carrondo, M.A.
Structure of Dimeric Cytochrome C3 from Desulfovibrio Gigas at 1.2 A Resolution
Acta Crystallogr.,Sect.D, 59:644-, 2003

PubMed Abstract: The structure of dimeric cytochrome c(3) from the sulfate-reducing bacterium Desulfovibrio gigas, diDg, obtained by ab initio methods was further refined to 1.2 A resolution, giving final reliability factors of R(free) = 14.8% and R = 12.4%. This cytochrome is a dimer of tetraheme cytochrome c(3) molecules covalently linked by two solvent-accessible disulfide bridges, a characteristic unique to members of the cytochrome c(3) superfamily. Anisotropic analysis using the semi-rigid TLS method shows different behaviour for analogous loops in each monomer arising from their different packing environments. A detailed sequence and structural comparison with all other known cytochrome c(3) domains in single- and multi-domain cytochromes c(3) shows the presence of structurally conserved regions in this family, despite the high variability of the amino-acid sequence. An internal water molecule is conserved in a common structural arrangement in all c(3) tetraheme domains, indicating a probable electron-transfer pathway between hemes I and II. Unique features of diDg are an internal methionine residue close to heme I and to one of the axial ligands of heme III, where all other structures of the cytochrome c(3) superfamily have a phenylalanine, and a rather unusual CXXXCH heme-binding motif only found so far in this cytochrome.

PubMed: 12657783
DOI: 10.1107/S090744490300194X

Experimental method

X-RAY DIFFRACTION (1.2 Å)